[Numpy-discussion] crash at prompt exit after running test

Charles R Harris charlesr.harris@gmail....
Tue Mar 9 23:27:31 CST 2010


On Tue, Mar 9, 2010 at 5:52 PM, Johann Cohen-Tanugi <cohen@lpta.in2p3.fr>wrote:

>  more fun :
> [cohen@jarrett tests]$ pwd
> /home/cohen/sources/python/numpy/numpy/core/tests
> [cohen@jarrett tests]$ python -c 'import test_ufunc'
>
> python: Modules/gcmodule.c:277: visit_decref: Assertion `gc->gc.gc_refs !=
> 0' failed.
> Aborted (core dumped)
>
> and in the debugger:
> (gdb) run
> Starting program: /usr/bin/python
> warning: .dynamic section for "/lib/libpthread.so.0" is not at the expected
> address
>
> warning: difference appears to be caused by prelink, adjusting expectations
> warning: .dynamic section for "/lib/libdl.so.2" is not at the expected
> address
>
> warning: difference appears to be caused by prelink, adjusting expectations
> warning: .dynamic section for "/lib/libc.so.6" is not at the expected
> address
>
> warning: difference appears to be caused by prelink, adjusting expectations
> [Thread debugging using libthread_db enabled]
>
> Python 2.6.2 (r262:71600, Jan 25 2010, 18:46:45)
> [GCC 4.4.2 20091222 (Red Hat 4.4.2-20)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import test_ufunc
>
> >>>
> >>>
> python: Modules/gcmodule.c:277: visit_decref: Assertion `gc->gc.gc_refs !=
> 0' failed.
>
> Program received signal SIGABRT, Aborted.
> 0x00aab416 in __kernel_vsyscall ()
> Missing separate debuginfos, use: debuginfo-install
> atlas-3.8.3-12.fc12.i686 libgcc-4.4.3-4.fc12.i686
> libgfortran-4.4.3-4.fc12.i686
> (gdb) bt
> #0  0x00aab416 in __kernel_vsyscall ()
> #1  0x00159a91 in raise (sig=6) at
> ../nptl/sysdeps/unix/sysv/linux/raise.c:64
> #2  0x0015b35a in abort () at abort.c:92
> #3  0x00152be8 in __assert_fail (assertion=<value optimized out>,
> file=<value optimized out>, line=<value optimized out>, function=<value
> optimized out>) at assert.c:81
> #4  0x0050931e in visit_decref (op=<value optimized out>, data=<value
> optimized out>) at Modules/gcmodule.c:277
> #5  0x0047c8c2 in dict_traverse (op=<value optimized out>, visit=<value
> optimized out>, arg=<value optimized out>) at Objects/dictobject.c:2003
> #6  0x00509af3 in subtract_refs (generation=<value optimized out>) at
> Modules/gcmodule.c:296
>
> #7  collect (generation=<value optimized out>) at Modules/gcmodule.c:817
> #8  0x0050a640 in PyGC_Collect () at Modules/gcmodule.c:1292
> #9  0x004fb0f0 in Py_Finalize () at Python/pythonrun.c:424
> #10 0x0050868f in Py_Main (argc=<value optimized out>, argv=<value
> optimized out>) at Modules/main.c:625
> #11 0x080485c8 in main (argc=<value optimized out>, argv=<value optimized
> out>) at Modules/python.c:23
>
> which looks identical to the bt I sent to Robert earlier on.
>
> HTH,
> Johann
>
>
> On 03/10/2010 12:43 AM, Johann Cohen-Tanugi wrote:
>
>
>
> On 03/10/2010 12:33 AM, Johann Cohen-Tanugi wrote:
>
>
>
> On 03/10/2010 12:07 AM, Pauli Virtanen wrote:
>
> ti, 2010-03-09 kello 21:14 +0100, Johann Cohen-Tanugi kirjoitti:
>
>
>  thinking about it, this morning there was a fedora update to python, so
> I am using 2.6.2-4.fc12.
> Looks like the problem is in python itself, hence this piece of info.
>
>
>  That the problem would be in Python is not so clear to me. Can you try
> running it with the previous Python shipped by Fedora? Do you see the
> problem then? What's the previous version, btw?
>
>
>  2.6.2-1 IIRC. I would have to check, and I am not sure how to either query
> this information or step back one update up with yum :(
>
> Memory errors are somewhat difficult to debug. Can you try running only
> a certain subset of the tests, first
>
> 	nosetests numpy.core
>
>
>  crash
>
> Be sure to set Pythonpath so that you get the correct Numpy version. If
> it segfaults, proceed to (under numpy/core/tests)
>
> 	nosetests test_multiarray.py
> 	nosetests test_multiarray.py:TestNewBufferProtocol
>
>
>  neither crash, so the problem is not there....
>
> I followed your lead and tried each script and ended up with :
> [cohen@jarrett tests]$ nosetests test_ufunc.py
> .............
> ----------------------------------------------------------------------
> Ran 13 tests in 1.146s
>
> OK
> python: Modules/gcmodule.c:277: visit_decref: Assertion `gc->gc.gc_refs !=
> 0' failed.
> Aborted (core dumped)
>
> so test_ufunc.py seems to be at stake
>
>  Since the crash occurs in cyclic garbage collection, I'm doubting a bit
> the numpy/core/src/multiarray/numpymemoryview.c implementation, since
> that's the only part in Numpy that supports that.
>
> Alternatively, just replace numpymemoryview.c with the attached one
> which has cyclic GC stripped, and see if you still get the crash.
>
> Cheers,
> Pauli
>
>
>
>
>
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Python 2.6.2 is rather old by now, the bugfix releases are up to 2.6.4. I
don't know that that is related, but I haven't seen any crashes on ubuntu
with 2.6.4.

Chuck
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